[Bioperl-l] How to extract xref information from seq object that is fetched from GenBank?

Sang Chul Choi goshng at gmail.com
Wed Aug 30 15:25:12 EDT 2006


Hi,

I am trying to fetch protein-coding DNA sequence from the public database.
I used Bio::DB::GenBank to fetch firstly protein sequence using SwissProt ID
or GenBank ID. Then, I am trying to look for DBSOURCE, which points to
where I can fetch the DNA sequence. But, I don't know how to get that
information.
Often, there are many links in 'xrefs' of DBSOURCE. For example,
---------------------
DBSOURCE    swissprot: locus CYSJ_ECOLI, accession P38038;
            class: standard.
            extra accessions:P14782,Q2MA65,created: Oct 1, 1994.
            sequence updated: Jun 27, 2006.
            annotation updated: Jun 27, 2006.
            xrefs: M23008.1, AAA23650.1, U29579.1, AAA69274.1, U00096.2,
            AAC75806.1, AP009048.1, BAE76841.1, H65057, 1DDGA, 1DDGB, 1DDIA,
            1YKGA
----------------------

I thought I could use Annotation object like this to have information
of DBSOURCE,
but I am starting to think I may be wrong because I could not get that DBSOURCE
information using Annoation object.

----------------------------------------
use Bio::DB::GenBank;
$gb = new Bio::DB::GenBank;

$seq = $gp->get_Seq_by_acc('P38038');
$ann_coll = $seq->annotation;
for $ann ($ann_coll->get_Annotations) {
   print $ann->tagname, " ", $ann->as_text, "\n";
}
----------------------------------------

How can I get this DBSOURCE information?

Thank you,

Sang Chul

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